Biological Problems (biological + problem)

Distribution by Scientific Domains

Selected Abstracts

Current trends in quantitative proteomics

Monica H. Elliott
Abstract It was inevitable that as soon as mass spectrometrists were able to tell biologists which proteins were in their samples, the next question would be how much of these proteins were present. This has turned out to be a much more challenging question. In this review, we describe the multiple ways that mass spectrometry has attempted to address this issue, both for relative quantitation and for absolute quantitation of proteins. There is no single method that will work for every problem or for every sample. What we present here is a variety of techniques, with guidelines that we hope will assist the researcher in selecting the most appropriate technique for the particular biological problem that needs to be addressed. We need to emphasize that this is a very active area of proteomics research,new quantitative methods are continuously being introduced and some ,pitfalls' of older methods are just being discovered. However, even though there is no perfect technique,and a better technique may be developed tomorrow,valuable information on biomarkers and pathways can be obtained using these currently available methods Copyright 2009 John Wiley & Sons, Ltd. [source]

Biological roles of translesion synthesis DNA polymerases in eubacteria

Dan I. Andersson
Summary Biological systems are strongly selected to maintain the integrity of their genomes by prevention and repair of external and internal DNA damages. However, some types of DNA lesions persist and might block the replication apparatus. The universal existence of specialized translesion synthesis DNA polymerases (TLS polymerases) that can bypass such lesions in DNA implies that replication blockage is a general biological problem. We suggest that the primary function for which translesion synthesis polymerases are selected is to rescue cells from replication arrest at lesions in DNA, a situation that, if not amended, is likely to cause an immediate and severe reduction in cell fitness and survival. We will argue that the mutagenesis observed during translesion synthesis is an unavoidable secondary consequence of this primary function and not, as has been suggested, an evolved mechanism to increase mutation rates in response to various stresses. Finally, we will discuss recent data on additional roles for translesion synthesis polymerases in the formation of spontaneous deletions and in transcription-coupled TLS, where the coupling of transcription to TLS is proposed to allow the rescue of the transcription machinery arrested at DNA lesions. [source]

Budding dispersal and the sex ratio

A. Gardner
Abstract There is much interest in understanding how population demography impacts upon social evolution. Here, we consider the impact of rate and pattern of dispersal upon a classic social evolutionary trait , the sex ratio. We recover existing analytical results for individual dispersal, and we extend these to allow for budding dispersal. In particular, while a cancelling of relatedness and kin competition effects means that the sex ratio is unaffected by the rate of individual dispersal, we find that a decoupling of relatedness and kin competition means that budding dispersal favours increasingly female-biased sex ratios. More generally, our analysis illustrates the relative ease with which biological problems involving class structure can be solved using a kin selection approach to social evolution theory. [source]

3D reconstruction of high-resolution STED microscope images

Annedore Punge
Abstract Tackling biological problems often involves the imaging and localization of cellular structures on the nanometer scale. Although optical super-resolution below 100 nm can be readily attained with stimulated emission depletion (STED) and photoswitching microscopy methods, attaining an axial resolution <100 nm with focused light generally required the use of two lenses in a 4Pi configuration or exceptionally bright photochromic fluorophores. Here, we describe a simple technical solution for 3D nanoscopy of fixed samples: biological specimens are fluorescently labeled, embedded in a polymer resin, cut into thin sections, and then imaged via STED microscopy with nanoscale resolution. This approach allows a 3D image reconstruction with a resolution <80 nm in all directions using available state-of-the art STED microscopes. Microsc. Res. Tech., 2008. 2008 Wiley-Liss, Inc. [source]

Current state and prospects of macromolecular crystallography

Zbigniew Dauter
The current situation and possible future development of macromolecular crystallography are reviewed. The rapid progress and maturation of this field in recent years have to a large extent been made possible by the inspiration and generous support of several active structural genomics initiatives. Two tendencies can be currently observed: one which treats protein crystallography as a highly automatic tool for investigating various biological problems without the need to engage in the intricacies of the technique and a second approach where this method is applied to crystals of difficult, large and complex biological systems, requiring a deeper knowledge of various aspects of crystallography. In the near future it is expected that these two trends will coexist, developing in a parallel fashion. [source]

An Introduction to Simulation and Visualization of Biological Systems at Multiple Scales: A Summer Training Program for Interdisciplinary Research

Rajan Munshi
Advances in biomedical research require a new generation of researchers having a strong background in both the life and physical sciences and a knowledge of computational, mathematical, and engineering tools for tackling biological problems. The NIH-NSF Bioengineering and Bioinformatics Summer Institute at the University of Pittsburgh (BBSI @ Pitt; is a multi-institutional 10-week summer program hosted by the University of Pittsburgh, Duquesne University, the Pittsburgh Supercomputing Center, and Carnegie Mellon University, and is one of nine Institutes throughout the nation currently participating in the NIH-NSF program. Each BBSI focuses on a different area; the BBSI @ Pitt, entitled "Simulation and Computer Visualization of Biological Systems at Multiple Scales", focuses on computational and mathematical approaches to understanding the complex machinery of molecular-to-cellular systems at three levels, namely, molecular, subcellular (microphysiological), and cellular. We present here an overview of the BBSI@Pitt, the objectives and focus of the program, and a description of the didactic training activities that distinguish it from other traditional summer research programs. Furthermore, we also report several challenges that have been identified in implementing such an interdisciplinary program that brings together students from diverse academic programs for a limited period of time. These challenges notwithstanding, presenting an integrative view of molecular-to-system analytical models has introduced these students to the field of computational biology and has allowed them to make an informed decision regarding their future career prospects. [source]